Akhtar ran against Gemma Tumelty to be President of the National Union of Students, becoming the first Muslim to run for this position, but lost amidst controversy involving Islamophobia and homophobia. . After The Guardian newspaper repeated the fact that Akhtar is gay, some users of the Muslim Public Affairs Committee forum voiced their contempt towards him . Akhtar told PinkNews.co.uk: “both Islamophobia and homophobia played a part in the election campaign.” He claims that some Muslim students were told: “don't vote for Pav, he's gay.” Although a member of the Labour Party, Akhtar was not a member of its student wing and ran for NUS President as an independent candidate.

Pav Akhtar was re-elected in May 2006 as Black Members’ Officer for the Labour Campaign for Lesbian & Gay Rights. And in June 2006, he was re-elected as Black students’ rep for the NUS LGBT Campaign.